2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.schemes;
21 import jalview.analysis.SequenceIdMatcher;
22 import jalview.datamodel.AlignmentAnnotation;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.AnnotatedCollectionI;
25 import jalview.datamodel.Annotation;
26 import jalview.datamodel.SequenceCollectionI;
27 import jalview.datamodel.SequenceI;
28 import jalview.io.TCoffeeScoreFile;
30 import java.awt.Color;
31 import java.util.ArrayList;
32 import java.util.IdentityHashMap;
34 import java.util.TreeMap;
37 * Defines the color score for T-Coffee MSA
39 * See http://tcoffee.org
42 * @author Paolo Di Tommaso
45 public class TCoffeeColourScheme extends ResidueColourScheme
48 static final Color[] colors =
49 { new Color(102, 102, 255), // #6666FF
50 new Color(0, 255, 0), // #00FF00
51 new Color(102, 255, 0), // #66FF00
52 new Color(204, 255, 0), // #CCFF00
53 new Color(255, 255, 0), // #FFFF00
54 new Color(255, 204, 0), // #FFCC00
55 new Color(255, 153, 0), // #FF9900
56 new Color(255, 102, 0), // #FF6600
57 new Color(255, 51, 0), // #FF3300
58 new Color(255, 34, 0) // #FF2000
61 IdentityHashMap<SequenceI, Color[]> seqMap;
64 * the color scheme needs to look at the alignment to get and cache T-COFFEE
68 * - annotated sequences to be searched
70 public TCoffeeColourScheme(AnnotatedCollectionI alignment)
72 alignmentChanged(alignment, null);
76 public void alignmentChanged(AnnotatedCollectionI alignment,
77 Map<SequenceI, SequenceCollectionI> hiddenReps)
79 // TODO: if sequences have been represented and they have scores, could
80 // compute an average sequence score for the representative
82 // assume only one set of TCOFFEE scores - but could have more than one
84 ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
85 // Search alignment to get all tcoffee annotation and pick one set of
86 // annotation to use to colour seqs.
87 seqMap = new IdentityHashMap<SequenceI, Color[]>();
88 AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
90 for (AlignmentAnnotation al : alcontext
91 .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
93 if (al.sequenceRef != null && !al.belowAlignment)
96 if (w < al.annotations.length)
98 w = al.annotations.length;
100 Color[] scores = new Color[al.annotations.length];
102 for (Annotation an : al.annotations)
104 scores[i++] = (an != null) ? an.colour : Color.white;
106 seqMap.put(al.sequenceRef, scores);
109 // TODO: compute average colour for each symbol type in each column - gives
110 // a second order colourscheme for colouring a sequence logo derived from
111 // the alignment (colour reflects quality of alignment for each residue
116 public Color findColour(char c, int j, SequenceI seq)
120 if (seqMap == null || (cols = seqMap.get(seq)) == null)
122 // see above TODO about computing a colour for each residue in each
123 // column: cc = _rcols[i][indexFor[c]];
127 if (j < 0 || j >= cols.length)
135 public ColourSchemeI applyTo(AnnotatedCollectionI sg,
136 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
138 return new TCoffeeColourScheme(sg);